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Ashish Kumar Tewari Rashi Gulshan Wadhwa Sanjeev Kumar Sharma Chakresh Kumar Jain 《Bioinformation》2013,9(2):112-115
Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to
promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror
attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The
architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows
platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10
microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines
designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources
and literature mining in order to provide the user with a comprehensive information system.
Availability
The database is freely available at http://www.bioterrorism.biowaves.org 相似文献2.
代谢网络定量分析研究进展 总被引：3，自引：0，他引：3
综述了代谢工程中代谢控制分析、代谢通量分析、生化系统理论、途径分析、控制论模型等定量分析方法的基本理论,以实例说明了这些方法的应用,并对代谢分析方法的发展进行了展望。 相似文献
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da Silveira NJ Bonalumi CE Uchõa HB Pereira JH Canduri F de Azevedo WF 《Cell biochemistry and biophysics》2006,44(3):366-374
Genome sequencing efforts are providing us with complete genetic blueprints for hundreds of organisms. We are now faced with
assigning, understanding, and modifying the functions of proteins encoded by these genomes. DBMODELING is a relational database
of annotated comparative protein structure models and their metabolic pathway characterization, when identified. This procedure
was applied to complete genomes such as Mycobacterium tuberculosis and Xylella fastidiosa. The main interest in the study of metabolic pathways is that some of these pathways are not present in humans, which makes
them selective targets for drug design, decreasing the impact of drugs in humans. In the database, there are currently 1116
proteins from two genomes. It can be accessed by any researcher at http://www. biocristalografia.df.ibilce. unesp.br/tools/.
This project confirms that homology modeling is a useful tool in structural bioinformatics and that it can be very valuable
in annotating genome sequence information, contributing to structural and functional genomics, and analyzing protein-ligand
docking. 相似文献
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Minoru Kanehisa 《Quantitative Biology.》2013,1(3):192
The KEGG pathway maps are widely used as a reference data set for inferring high-level functions of the organism or the ecosystem from its genome or metagenome sequence data. The KEGG modules, which are tighter functional units often corresponding to subpathways in the KEGG pathway maps, are designed for better automation of genome interpretation. Each KEGG module is represented by a simple Boolean expression of KEGG Orthology (KO) identifiers (K numbers), enabling automatic evaluation of the completeness of genes in the genome. Here we focus on metabolic functions and introduce reaction modules for improving annotation and signature modules for inferring metabolic capacity. We also describe how genome annotation is performed in KEGG using the manually created KO database and the computationally generated SSDB database. The resulting KEGG GENES database with KO (K number) annotation is a reference sequence database to be compared for automated annotation and interpretation of newly determined genomes. 相似文献
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Young JD Henne KL Morgan JA Konopka AE Ramkrishna D 《Biotechnology and bioengineering》2008,100(3):542-559
Cybernetic modeling strives to uncover the inbuilt regulatory programs of biological systems and leverage them toward computational prediction of metabolic dynamics. Because of its focus on incorporating the global aims of metabolism, cybernetic modeling provides a systems-oriented approach for describing regulatory inputs and inferring the impact of regulation within biochemical networks. Combining cybernetic control laws with concepts from metabolic pathway analysis has culminated in a systematic strategy for constructing cybernetic models, which was previously lacking. The newly devised framework relies upon the simultaneous application of local controls that maximize the net flux through each elementary flux mode and global controls that modulate the activities of these modes to optimize the overall nutritional state of the cell. The modeling concepts are illustrated using a simple linear pathway and a larger network representing anaerobic E. coli central metabolism. The E. coli model successfully describes the metabolic shift that occurs upon deleting the pta-ackA operon that is responsible for fermentative acetate production. The model also furnishes predictions that are consistent with experimental results obtained from additional knockout strains as well as strains expressing heterologous genes. Because of the stabilizing influence of the included control variables, the resulting cybernetic models are more robust and reliable than their predecessors in simulating the network response to imposed genetic and environmental perturbations. 相似文献
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组学分析技术的发展推动生物学逐渐成为一门以数据分析为中心的科学。依托生物数据在细胞整体系统水平建立数字细胞模型,对于理解细胞系统组织原理和生命产生进化规律,预测各种环境和基因扰动对细胞功能的影响并指导设计人工生命具有重要意义,因此数字细胞的构建模拟设计已成为合成生物学的核心研究内容与底层支撑技术。本文重点对天津工业生物技术研究所创立十年来在数字细胞研究方面的进展进行回顾介绍,重点包括基因组尺度代谢网络模型的构建、质控以及其在途径设计和指导菌种代谢工程改造方面的应用,进一步结合近年来细胞模型研究的前沿趋势,对整合多种约束的模型的构建和分析研究方面的最新成果进行了介绍,最后对数字细胞研究的未来发展方向进行展望。数字细胞技术将与基因组测序、合成和编辑等合成生物学前沿技术一起提升人们对生命进行读写改创的能力。 相似文献
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A stoichiometric model of Acidithiobacillus ferrooxidans based on the sequenced genome from strain ATCC 23270 is derived and parameterized using genome/pathway databases. The model describes the main aspects of catabolism and anabolism. By the construction and utilization of the mathematical determination of the network, metabolic flux analysis is performed for such a bacterium for the first time and results are successfully verified by comparison to literature values. This first metabolic model of A. ferrooxidans is able to simulate the main aspects of metabolism and will be useful for further investigation and improvement of bioleaching procedures. Biotechnol. Bioeng. 2009;102: 1448–1459. © 2008 Wiley Periodicals, Inc. 相似文献
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基元模式分析是应用最广泛的代谢途径分析方法。基元模式分析的研究对象从代谢网络发展到信号传导网络;研究尺度从细胞到生物反应器,甚至生态系统;数学描述从稳态分解到动态解析;研究领域从微生物代谢到人类疾病。以下综述了基元模式分析的算法和软件开发现状,以及其在代谢途径与鲁棒性、代谢通量分解、稳态代谢通量分析、动态模型与生物过程模拟、网络结构与调控、菌株设计和信号传导网络等方面的应用。开发新的算法解决组合爆炸问题,探索基元模式与代谢调控的关系以及提高菌株设计算法效率是今后基元模式的重要发展方向。 相似文献
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Yen-An Lu Conor M. O' Brien Douglas G. Mashek Wei-Shou Hu Qi Zhang 《Biotechnology and bioengineering》2023,120(1):216-229
Over the last two decades, model-based metabolic pathway optimization tools have been developed for the design of microorganisms to produce desired metabolites. However, few have considered more complex cellular systems such as mammalian cells, which requires the use of nonlinear kinetic models to capture the effects of concentration changes and cross-regulatory interactions. In this study, we develop a new two-stage pathway optimization framework based on kinetic models that incorporate detailed kinetics and regulation information. In Stage 1, a set of optimization problems are solved to identify and rank the enzymes that contribute the most to achieving the metabolic objective. Stage 2 then determines the optimal enzyme interventions for specified desired numbers of enzyme adjustments. It also incorporates multi-scenario optimization, which allows the simultaneous consideration of multiple physiological conditions. We apply the proposed framework to find enzyme adjustments that enable a reverse glucose flow in cultured mammalian cells, thereby eliminating the need for glucose feed in the late culture stage and enhancing process robustness. The computational results demonstrate the efficacy of the proposed approach; it not only captures the important regulations and key enzymes for reverse glycolysis but also identifies differences and commonalities in the metabolic requirements for different carbon sources. 相似文献
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聚磷菌是一类非常重要的工程菌,广泛应用于污水处理厂生物除磷过程。聚磷菌可以吸收超过自身所能利用的数倍的磷,在体内合成聚磷化合物从而达到生物除磷的目的。在过去的几年里,宏基因组学以及测序技术的发展大大推动了对聚磷菌物种组成及其磷代谢过程的认识。本文主要对宏基因组技术进行介绍并对近几年基于宏基因组技术深入研究聚磷菌的文章进行综述,以期对这类重要的微生物的生理功能、代谢途径和物种多样性进行全面的了解。 相似文献
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化石燃料生物脱有机氮研究展望 总被引：2，自引：0，他引：2
化石燃料中与有机硫相似的另一类孤对电子含氮有机化合物的存在对生产和环境造成许多危害。石油中的含氮有机化合物是影响炼油工艺、产品性能质量的主要因素。含氮有机化合物具有致癌、致突变性 ,燃烧后则以NOx的形式释放污染大气。化石燃料中所含的有机氮较有机硫更难以去除 ,常规的化学脱有机氮技术高压加氢法处理燃油能耗高 ,处理效果不理想等方面的缺陷使人们思考生物脱氮的可能性。考察了国内外近十多年来化石燃料生物脱有机氮工作的研究进展 ,包括模式有机氮化合物微生物的代谢途径 ,以及相应的代谢途径中的关键酶及其编码基因等方面的研究。 相似文献
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Sowmiya Balasubramanian 《Biocatalysis and Biotransformation》2019,37(4):310-316
Engineering microbes with heterologous pathway for production of bio-based products has received considerable attention. Reconstituting such non-native pathway in addition to desired product formation often brings an allosteric modulation in enzymes competing at fragile nodes that result in by-product redistribution, in order to retain energy and redox balance. This work, Lactobacillus plantarum engineered with acrylate pathway for propionate production was studied under similar perspectives. Upon expression, the heterologous pathway did not result in propionic acid production under standard glucose concentration of 20?g/L, but 0.01?mM of propionate was formed when grown under low glucose concentration of 1?g/L. Further analysis of secreted metabolites with increased glucose concentration of 10 and 30?g/L remained futile towards propionate formation but showed reorientation in pyruvate metabolism which was related to the control imposed by the host to regulate the hidden constraints caused by gene perturbation. Further, it was ensured that the limitation of supplements did not play any functional role in inhibiting propionic acid synthesis but still followed similar metabolic pattern which was quite unclear though interpreted to certain extent. Thus, the findings gave insights into physiological and metabolic capabilities of Lactobacillus plantarum that at least in principle can be used to enhance the strain performance for increased propionic acid production. 相似文献
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Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker‐driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end‐users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post‐acquisition analysis of proteomic data. 相似文献
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Hiroyuki Sonoda Haku Iizuka Sho Ishiwata Daisuke Tsunoda Masako Abe Kenji Takagishi Hirotaka Chikuda Noriyuki Koibuchi Noriaki Shimokawa 《Journal of cellular biochemistry》2019,120(9):15007-15017
Although congenital scoliosis is defined as a genetic disease characterized by a congenital and abnormal curvature of the spinal vertebrae, our knowledge of the genetic underpinnings of the disease is insufficient. We herein show that the downregulation of the retinol-retinoic acid metabolism pathway is involved in the pathogenesis of congenital scoliosis. By analyzing DNA microarray data, we found that the expression levels of genes associated with the retinol metabolism pathway were decreased in the lumbar spine of Ishibashi rats (IS), a rat model of congenital kyphoscoliosis. The expression of Adh1 and Aldh1a2 (alcohol dehydrogenase), two enzymes that convert retinol to retinoic acid in this pathway, were decreased at both the gene and protein levels. Rarα, a receptor of retinoic acid and bone morphogenetic protein 2, which play a central role in bone formation and are located downstream of this pathway, were also downregulated. Interestingly, the serum retinol levels of IS rats were higher than those of wild-type control rats. These results indicate that the adequate conversion from retinol to retinoic acid is extremely important in the regulation of normal bone formation and it may also be a key factor for understanding the pathogenesis of congenital scoliosis. 相似文献